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1.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-323754

ABSTRACT

Background: The coronavirus disease-19 (COVID-19) and its variants have increased rapidly worldwide since December 2019, with respiratory disease being a prominent complication. As such, optimizing evaluation methods and identifying factors predictive of disease progress remain critical. The purpose of the study was to assess late phase (≥3 weeks) pulmonary changes using intensity-based computed tomography (CT) scoring in COVID-19 patients and determine the clinical characteristics predicting lung abnormalities and recovery. Methods: : We conducted a retrospective study on 42 patients (14 males, 28 females;age 65±10 years) with COVID-19. Only patients with at least 3 CT scans taken at least 3 weeks after initial symptom onset were included in the study. Two scoring methods were assessed: (1) area-based scoring (ABS) and (2) intensity-weighted scoring (IWS). Temporal changes in the average lung lesion were evaluated by the calculating the averaged area under the curve (AUC) of the CT score-time curve. Correlations between averaged AUCs and clinical characteristics were determined. Results: Using the ABS system, temporal changes in lung abnormalities during recovery were highly variable (P=0.934). By contrast, the IWS system detected more subtle changes in lung abnormalities during in COVID-19 patients, with consistent week-to-week relative reductions in IWS (P=0.025). Strong relationships were observed with D-dimer and C-reactive protein (CRP) levels on admission, with hazard ratios (HR)(95%CI) of 5.32 (1.25-22.6)(P=0.026) and 1.05 (1.10-1.09)(P=0.017), respectively. Conclusion: Our results suggest COVID-19-mediated pulmonary abnormalities persist well-beyond 3-weeks of symptom onset, with intensity-weighted rather than area-based scoring being more sensitive. Moreover, D-dimer and CRP levels were predictive of the recovery from the disease.

2.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-323753

ABSTRACT

Objectives: To assess the late phase CT changes of COVID-19 patients, and figure out factors predicting lung abnormality in late phase. Methods: : We conducted a retrospective study on 42 patients (14 males, 28 females;age 65±10 years) with COVID-19 admitted between February 7, 2020 and March 27, 2020. Only patients with at least 3 CT scans taken at least 3 weeks after initial symptom onset were included in the study. CT images were analyzed by 2 independent radiologists using different scoring: (1) area-based scoring (ABS);and (2) intensity-weighted scoring (IWS). Temporal changes in the average lung lesion were evaluated by averaged area under the curve (AUC) of the CT score-time curve. Correlations between averaged AUCs and clinical characteristics were determined. Results: Temporal changes in lung abnormalities during recovery (weeks 3 through 8) of CT findings using the ABS system were variable (P=0.934). By contrast, the IWS system detected more subtle changes in lung abnormalities during the late phase of recovery in COVID-19 patients, with consistent week-to-week relative reductions in IWS (P=0.025). In assessing the correlation between averaged AUCs and clinical characteristics, strong relationships were observed with D-dimer and C-reactive protein (CRP) levels on admission, with hazard ratios (HR)(95%CI) of 5.32 (1.25-22.6)(P=0.026) and 1.05 (1.10-1.09)(P=0.017), respectively. Conclusion: Our results suggest an intensity-weighted rather than area-based scoring system is more sensitive to detect subtle temporal CT changes in COVID-19, with D-dimer and CRP levels on admission being predictive of the time course of late phase recovery from the disease.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-325167

ABSTRACT

We present a large, challenging dataset, COUGH, for COVID-19 FAQ retrieval. Similar to a standard FAQ dataset, COUGH consists of three parts: FAQ Bank, Query Bank and Relevance Set. The FAQ Bank contains ~16K FAQ items scraped from 55 credible websites (e.g., CDC and WHO). For evaluation, we introduce Query Bank and Relevance Set, where the former contains 1,236 human-paraphrased queries while the latter contains ~32 human-annotated FAQ items for each query. We analyze COUGH by testing different FAQ retrieval models built on top of BM25 and BERT, among which the best model achieves 48.8 under P@5, indicating a great challenge presented by COUGH and encouraging future research for further improvement. Our COUGH dataset is available at https://github.com/sunlab-osu/covid-faq.

5.
CMAJ ; 192(48): E1648-E1656, 2020 Nov 30.
Article in French | MEDLINE | ID: covidwho-1094079

ABSTRACT

CONTEXTE: Les atteintes cardiaques sont fréquentes dans les cas graves de maladie à coronavirus 2019 (COVID-19) et sont associées à un mauvais pronostic. Notre étude portait sur les facteurs prédictifs de mortalité intrahospitalière, les caractéristiques de l'arythmie et les effets des traitements qui allongent l'intervalle QT chez les patients ayant une atteinte cardiaque. MÉTHODES: Nous avons fait une étude de cohorte rétrospective des cas graves de COVID-19 admis à l'hôpital Tongji, à Wuhan, en Chine, entre le 29 janvier et le 8 mars 2020. En examinant ceux qui avaient une atteinte cardiaque, définie ici comme un taux élevé de troponine I cardiaque (TnIc), nous avons déterminé les caractéristiques biologiques et cliniques associées à la mortalité et au besoin de ventilation invasive. RÉSULTATS: Parmi les 1284 cas graves de COVID-19, 1159 avaient au dossier un taux de TnIc mesuré à l'admission, qui pour 170 (14,7 %) participants indiquait une atteinte cardiaque. Les patients ayant une atteinte cardiaque avaient un taux de mortalité nettement plus élevé que les autres patients (71,2 % c. 6,6 %; p < 0,001). Nous avons constaté que le taux de TnIc initial (pour chaque augmentation d'un facteur 10, rapport de risque [HR] 1,32, intervalle de confiance [IC] à 95 % 1,06­1,66) et le taux de TnIc maximal atteint au cours de la maladie (pour chaque augmentation d'un facteur 10, HR 1,70, IC à 95 % 1,38­2,10) étaient associés à de minces chances de survie. Le taux de TnIc maximal était aussi associé au besoin de ventilation invasive (rapport de cotes 3,02, IC à 95 % 1,92­4,98). Sur les 170 patients ayant une atteinte cardiaque, 44 (25,9 %) présentaient une arythmie. Les 6 qui souffraient de tachycardie ou de fibrillation ventriculaires sont morts. Nous avons remarqué que les patients qui recevaient des médicaments allongeant l'intervalle QT avaient un intervalle QTc plus long que ceux qui n'en recevaient pas (différence entre les médianes 45 ms; p = 0,01), mais que ce traitement n'était pas directement lié à la mortalité (HR 1,04, IC à 95 % 0,69­1,57). INTERPRÉTATION: Chez les patients ayant la COVID-19 et une atteinte cardiaque, les taux initial et maximal de TnIc sont associés à de minces chances de survie, et le taux maximal est un facteur prédictif du besoin de ventilation invasive. Les malades de la COVID-19 doivent subir un dépistage des atteintes cardiaques et être surveillés, surtout si on leur fait suivre un traitement qui peut prolonger la repolarisation. Enregistrement de l'essai : Registre des essais cliniques chinois, n° ChiCTR2000031301.

6.
Revista Romana de Medicina de Laborator ; 29(1):85-91, 2021.
Article in English | GIM | ID: covidwho-1082180

ABSTRACT

Background: Coronavirus disease 2019 (COVID-19) has spread rapidly in China and globally. In order to control the spread of the epidemic, it is important to find an efficient diagnostic method. Objectives: The aim of this study was to assess the responses of antibodies during SARS-CoV-2 infection in relation to disease severity and to evaluate the association between the positive rate of antibody detection and nucleic acid test.

7.
Proc Natl Acad Sci U S A ; 118(1)2021 01 05.
Article in English | MEDLINE | ID: covidwho-1066044

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global health. Although varied SARS-CoV-2-related coronaviruses have been isolated from bats and SARS-CoV-2 may infect bat, the structural basis for SARS-CoV-2 to utilize the human receptor counterpart bat angiotensin-converting enzyme 2 (bACE2) for virus infection remains less understood. Here, we report that the SARS-CoV-2 spike protein receptor binding domain (RBD) could bind to bACE2 from Rhinolophus macrotis (bACE2-Rm) with substantially lower affinity compared with that to the human ACE2 (hACE2), and its infectivity to host cells expressing bACE2-Rm was confirmed with pseudotyped SARS-CoV-2 virus and SARS-CoV-2 wild virus. The structure of the SARS-CoV-2 RBD with the bACE2-Rm complex was determined, revealing a binding mode similar to that of hACE2. The analysis of binding details between SARS-CoV-2 RBD and bACE2-Rm revealed that the interacting network involving Y41 and E42 of bACE2-Rm showed substantial differences with that to hACE2. Bats have extensive species diversity and the residues for RBD binding in bACE2 receptor varied substantially among different bat species. Notably, the Y41H mutant, which exists in many bats, attenuates the binding capacity of bACE2-Rm, indicating the central roles of Y41 in the interaction network. These findings would benefit our understanding of the potential infection of SARS-CoV-2 in varied species of bats.


Subject(s)
Angiotensin-Converting Enzyme 2 , COVID-19/genetics , COVID-19/metabolism , Chiroptera , SARS-CoV-2 , Amino Acid Substitution , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , Animals , COVID-19/epidemiology , Chiroptera/genetics , Chiroptera/metabolism , Chiroptera/virology , HEK293 Cells , Humans , Mutation, Missense , Pandemics , Protein Binding , Protein Domains , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Species Specificity
8.
Proc Natl Acad Sci U S A ; 118(1)2021 01 05.
Article in English | MEDLINE | ID: covidwho-990135

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global health. Although varied SARS-CoV-2-related coronaviruses have been isolated from bats and SARS-CoV-2 may infect bat, the structural basis for SARS-CoV-2 to utilize the human receptor counterpart bat angiotensin-converting enzyme 2 (bACE2) for virus infection remains less understood. Here, we report that the SARS-CoV-2 spike protein receptor binding domain (RBD) could bind to bACE2 from Rhinolophus macrotis (bACE2-Rm) with substantially lower affinity compared with that to the human ACE2 (hACE2), and its infectivity to host cells expressing bACE2-Rm was confirmed with pseudotyped SARS-CoV-2 virus and SARS-CoV-2 wild virus. The structure of the SARS-CoV-2 RBD with the bACE2-Rm complex was determined, revealing a binding mode similar to that of hACE2. The analysis of binding details between SARS-CoV-2 RBD and bACE2-Rm revealed that the interacting network involving Y41 and E42 of bACE2-Rm showed substantial differences with that to hACE2. Bats have extensive species diversity and the residues for RBD binding in bACE2 receptor varied substantially among different bat species. Notably, the Y41H mutant, which exists in many bats, attenuates the binding capacity of bACE2-Rm, indicating the central roles of Y41 in the interaction network. These findings would benefit our understanding of the potential infection of SARS-CoV-2 in varied species of bats.


Subject(s)
Angiotensin-Converting Enzyme 2 , COVID-19/genetics , COVID-19/metabolism , Chiroptera , SARS-CoV-2 , Amino Acid Substitution , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , Animals , COVID-19/epidemiology , Chiroptera/genetics , Chiroptera/metabolism , Chiroptera/virology , HEK293 Cells , Humans , Mutation, Missense , Pandemics , Protein Binding , Protein Domains , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Species Specificity
9.
J Clin Lab Anal ; 35(1): e23654, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-932443

ABSTRACT

BACKGROUND: Geriatric patients with coronavirus disease (COVID-19) are at high risk of developing cardiac injury. Identifying the factors that affect high-sensitivity cardiac troponin I may indicate the cause of cardiac injury in elderly patients, and this could hopefully assist in protecting heart function in this patient population. METHODS: One hundred and eighty inpatients who were admitted for COVID-19 were screened. Patients older than 60 years were included in this study, and the clinical characteristics and laboratory results of the cohort were analyzed. The correlation between cardiac injury and clinical/laboratory variables was statistically analyzed, and further logistic regression was performed to determine how these variables influence cardiac injury in geriatric patients. RESULTS: Age (p < 0.001) significantly correlated with cardiac injury, whereas sex (p = 0.372) and coexisting diseases did not. Rising procalcitonin (p = 0.001), interleukin-2 receptor (p < 0.001), interleukin 6 (p = 0.001), interleukin 10 (p < 0.001), tumor necrosis factor α (p = 0.001), high-sensitivity C-reactive protein (p = 0.001), D-dimer (p < 0.001), white blood cells (p < 0.001), neutrophils (p = 0.001), declining lymphocytes (p < 0.001), and natural killer cells (p = 0.005) were associated with cardiac injury and showed predictive ability in the multivariate logistic regression. CONCLUSION: Our results suggest that age and inflammatory factors influence cardiac injury in elderly patients. Interfering with inflammation in this patient population may potentially confer cardiac protection.


Subject(s)
COVID-19/complications , Cardiomyopathies/virology , Aged , Aged, 80 and over , COVID-19/blood , Cardiomyopathies/etiology , Creatine Kinase/blood , Humans , Inflammation Mediators/blood , Killer Cells, Natural , L-Lactate Dehydrogenase/blood , Male , Middle Aged , Myocarditis/etiology , Myocarditis/virology , Natriuretic Peptide, Brain/blood , Peptide Fragments/blood , Risk Factors , Troponin T/blood
10.
Acta Veterinaria et Zootechnica Sinica ; 51(8):2027-2031, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-833202

ABSTRACT

The aim of this study was to investigate the infection of feline coronavirus (FCoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in partial areas of China during the novel coronavirus outbreak. Nose swabs and rectal swabs were collected from cats presented with respiratory disease symptoms and gastrointestinal disease symptoms in pet hospitals of 14 cities in China. Total RNAs were extracted from the samples and then were transcribed to cDNA. The FCoV and SARS-CoV-2 were detected by the reported PCR methods. As a result, no SARS-CoV-2 case has been detected in 269 cats, while there were 35 cats infected with feline coronavirus. It was suggested that there was no case infected with SARS-CoV-2 in fourteen cities in China during novel coronavirus outbreak.

12.
Nat Commun ; 11(1): 4417, 2020 09 04.
Article in English | MEDLINE | ID: covidwho-744372

ABSTRACT

COVID-19 was declared a pandemic on March 11 by WHO, due to its great threat to global public health. The coronavirus main protease (Mpro, also called 3CLpro) is essential for processing and maturation of the viral polyprotein, therefore recognized as an attractive drug target. Here we show that a clinically approved anti-HCV drug, Boceprevir, and a pre-clinical inhibitor against feline infectious peritonitis (corona) virus (FIPV), GC376, both efficaciously inhibit SARS-CoV-2 in Vero cells by targeting Mpro. Moreover, combined application of GC376 with Remdesivir, a nucleotide analogue that inhibits viral RNA dependent RNA polymerase (RdRp), results in sterilizing additive effect. Further structural analysis reveals binding of both inhibitors to the catalytically active side of SARS-CoV-2 protease Mpro as main mechanism of inhibition. Our findings may provide critical information for the optimization and design of more potent inhibitors against the emerging SARS-CoV-2 virus.


Subject(s)
Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Proline/analogs & derivatives , Protease Inhibitors/pharmacology , Pyrrolidines/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Animals , Antiviral Agents/pharmacology , Betacoronavirus/enzymology , Binding Sites/drug effects , COVID-19 , Catalytic Domain , Chlorocebus aethiops , Coronavirus 3C Proteases , Crystallography, X-Ray , Cysteine Endopeptidases/chemistry , Cysteine Endopeptidases/metabolism , Disease Models, Animal , High-Throughput Screening Assays , Models, Molecular , Pandemics , Proline/pharmacology , RNA-Dependent RNA Polymerase/antagonists & inhibitors , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/metabolism , SARS-CoV-2 , Sulfonic Acids , Vero Cells , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Virus Replication/drug effects
13.
CMAJ ; 192(28): E791-E798, 2020 07 13.
Article in English | MEDLINE | ID: covidwho-615109

ABSTRACT

BACKGROUND: Cardiac injury is common in severe coronavirus disease 2019 (COVID-19) and is associated with poor outcomes. We aimed to study predictors of in-hospital death, characteristics of arrhythmias and the effects of QT-prolonging therapy in patients with cardiac injury. METHODS: We conducted a retrospective cohort study involving patients with severe COVID-19 who were admitted to Tongji Hospital in Wuhan, China, between Jan. 29 and Mar. 8, 2020. Among patients who had cardiac injury, which we defined as an elevated level of cardiac troponin I (cTnI), we identified demographic and clinical characteristics associated with mortality and need for invasive ventilation. RESULTS: Among 1284 patients with severe COVID-19, 1159 had a cTnI level measured on admission to hospital, of whom 170 (14.7%) had results that showed cardiac injury. We found that mortality was markedly higher in patients with cardiac injury (71.2% v. 6.6%, p < 0.001). We determined that initial cTnI (per 10-fold increase, hazard ratio [HR] 1.32, 95% confidence interval [CI] 1.06-1.66) and peak cTnI level during illness (per 10-fold increase, HR 1.70, 95% CI 1.38-2.10) were associated with poor survival. Peak cTnI was also associated with the need for invasive ventilation (odds ratio 3.02, 95% CI 1.92-4.98). We found arrhythmias in 44 of the 170 patients with cardiac injury (25.9%), including 6 patients with ventricular tachycardia or fibrillation, all of whom died. We determined that patients who received QT-prolonging drugs had longer QTc intervals than those who did not receive them (difference in medians, 45 ms, p = 0.01), but such treatment was not independently associated with mortality (HR 1.04, 95% CI 0.69-1.57). INTERPRETATION: We found that in patients with COVID-19 and cardiac injury, initial and peak cTnI levels were associated with poor survival, and peak cTnI was a predictor of need for invasive ventilation. Patients with COVID-19 warrant assessment for cardiac injury and monitoring, especially if therapy that can prolong repolarization is started. TRIAL REGISTRATION: Chinese Clinical Trial Registry, No. ChiCTR2000031301.


Subject(s)
Arrhythmias, Cardiac/mortality , Arrhythmias, Cardiac/virology , Coronavirus Infections/mortality , Coronavirus Infections/physiopathology , Heart Injuries/mortality , Heart Injuries/virology , Patient Discharge/statistics & numerical data , Pneumonia, Viral/mortality , Pneumonia, Viral/physiopathology , Anti-Arrhythmia Agents/therapeutic use , Arrhythmias, Cardiac/blood , Betacoronavirus/pathogenicity , Biomarkers/blood , COVID-19 , China/epidemiology , Coronavirus Infections/blood , Coronavirus Infections/virology , Critical Illness , Heart Injuries/blood , Hospital Mortality , Humans , Intensive Care Units , Logistic Models , Pandemics , Pneumonia, Viral/blood , Pneumonia, Viral/virology , Prognosis , Respiration, Artificial/statistics & numerical data , Retrospective Studies , SARS-CoV-2 , Troponin I/blood
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